I'm not african, just a european with a pair of running shoes and a spirit of adventure !
My medical knowledge is patchy but i have never heard of contracting malaria from touching water. That said there are plenty of other things you can contract from touching water - bilhazia being one of the less pleasent. When i am at 8000ft there are very few mosquitos and certainly none of the malaria carrying kind. You should take medical advice from a pro.
The logistics is one of those things that when you have done it once you wonder what the fuss was about. Here are some suggestions:
You could conincide your flight with that of returning kenyan runners and get a lift with them. You will be welcome. Suggest you call one of the management companies who manage kenyans and ask nicely. In my experience athletes and managers are more than helpful when asked.
Alternatively email Lornah through her website and see when she has groups of people coming from nairobi.http://www.lornah.com/index.htm
You have to give it a go